Just to nitpick, there were a few typos in the question you posted, so here it is in the original form:
In an interview last month, the rebels estimated that a few hundred of their fighters had been trained over the past two years, and they received close to two million dollars worth of ammunition, guns, and heavy artillery during the same time period.
A) had been trained over the past two years, and they
B) were trained over the past two years, and they had
C) were trained over the past two years and they have
D) had been trained over the past two years and that they had
E) had been trained over the past two years and that they have
I only post it because "fighters" should be plural as it affects the question!
First step is to "cut the fat" -- here's the basic meaning of the sentence:
Rebels estimated that fighters had been trained, and they received.
There's two important things going on here: Parallelism and Meaning.
#1 - Parallelism. The GMAT LOVES Parallelism (LOVES it!) so whenever we see 1 noun doing the action of 2 verbs separated by "and," I'm always looking for ways to make those two verbs "parallel" (same tense). Here the verbs are "had been trained" and "received." One is in past perfect form, and the other is in simple past tense. Hmmm...the GMAT's not super into that. Red flag! It would be great if they were BOTH the same.
#2 - Meaning. The last phrase in the sentence states "during the same time period" so BOTH events described in the sentence (the training and the receiving of $$) happened at the same time. We usually only use past perfect tense to describe something that occurred even further back in the past than another past tense event.
For example: I went to store. I went to the movies.
Which one did I do first? We can't tell, because both are in past tense! That's annoying. But, throw a little past perfect in there:
I went to the store. I had gone to the movies.
And voila! Suddenly it's super clear that I went to the movies BEFORE I went to the store.
Anyway, long story short, because the sentence literally states these two events happened at the SAME time, they should both have the SAME tense. Only (D) does this by making them BOTH past perfect.
